conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense single-stranded RNA [(+)ssRNA] viruses and closely related viruses; This family contains the catalytic core domain of RdRp of RNA viruses which belong to Group IV of the Baltimore classification system, and are a group of related viruses that have positive-sense (+), single-stranded (ss) genomes made of ribonucleic acid (RNA). RdRp (also known as RNA replicase) catalyzes the replication of RNA from an RNA template; specifically, it catalyzes the synthesis of the RNA strand complementary to a given RNA template. The Baltimore Classification is divided into 7 classes, 3 of which include RNA viruses: Group IV (+) RNA viruses, Group III double-stranded (ds) RNA viruses, and Group V negative-sense (-) RNA viruses. Baltimore groups of viruses differ with respect to the nature of their genome (i.e., the nucleic acid form that is packaged into virions) and correspond to distinct strategies of genome replication and expression. (+) viral RNA is similar to mRNA and thus can be immediately translated by the host cell. (+)ssRNA viruses can also produce (+) copies of the genome from (-) strands of an intermediate dsRNA genome. This acts as both a transcription and a replication process since the replicated RNA is also mRNA. RdRps belong to the expansive class of polymerases containing so-called palm catalytic domains along with the accessory fingers and thumb domains. All RdRps also have six conserved structural motifs (A-F), located in its majority in the palm subdomain (A-E motifs) and the F motif is located on the finger subdomain. All these motifs have been shown to be implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. In addition to Group IV viruses, this model also includes Picobirnaviruses (PBVs), members of the family Picobirnaviridae of dsRNA viruses (Baltimore classification Group III), which are bi-segmented dsRNA viruses. The phylogenetic tree of the RdRps of RNA viruses (realm Riboviria) showed that picobirnaviruses are embedded in the branch of diverse (+)RNA viruses; sometimes they are collectively referred to as the picornavirus supergroup. RdRps of members of the family Permutatetraviridae, a distinct group of RNA viruses that encompass a circular permutation within the RdRp palm domain, are not included in this model.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172384890   1 MEKEGKISKIGpeNPYNTPVFAIKKKDS*KWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKK*SVTVLDVGDAYFSVPL 80
Cdd:cd01645    24 QLKEGHIEPST--SPWNTPVFVIKKKSG-KWRLLHDLRAVNAQTQDMGALQPGLPHPAALPKGWPLIVLDLKDCFFSIPL 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172384890  81 HEDFRKYTAFTIPSTNNETPGIRYQYNVLPQGWKGSPAIFQCSMTKILEPFRTQNPEIVIYQYMDDLYVGSDLEiGQHRK 160
Cdd:cd01645   101 HPDDRERFAFTVPSINNKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYPDIVIYHYMDDILIASDLE-GQLRE 179

                         170       180       190
                  ....*....|....*....|....*....|....
gi 1172384890 161 KVEELR*HLLKWGFTTP*KKHQKEPPFLWMGYEL 194
Cdd:cd01645   180 IYEELRQTLLRWGLTIPPEKVQKEPPFQYLGYEL 213

RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of single-stranded RNA into double-stranded viral DNA for integration into host chromosomes. Proteins in this subfamily contain long terminal repeats (LTRs) and are multifunctional enzymes with RNA-directed DNA polymerase, DNA directed DNA polymerase, and ribonuclease hybrid (RNase H) activities. The viral RNA genome enters the cytoplasm as part of a nucleoprotein complex, and the process of reverse transcription generates in the cytoplasm forming a linear DNA duplex via an intricate series of steps. This duplex DNA is colinear with its RNA template, but contains terminal duplications known as LTRs that are not present in viral RNA. It has been proposed that two specialized template switches, known as strand-transfer reactions or "jumps", are required to generate the LTRs.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172384890   1 MEKEGKISKIGpeNPYNTPVFAIKKKDS*KWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKK*SVTVLDVGDAYFSVPL 80
Cdd:cd01645    24 QLKEGHIEPST--SPWNTPVFVIKKKSG-KWRLLHDLRAVNAQTQDMGALQPGLPHPAALPKGWPLIVLDLKDCFFSIPL 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172384890  81 HEDFRKYTAFTIPSTNNETPGIRYQYNVLPQGWKGSPAIFQCSMTKILEPFRTQNPEIVIYQYMDDLYVGSDLEiGQHRK 160
Cdd:cd01645   101 HPDDRERFAFTVPSINNKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYPDIVIYHYMDDILIASDLE-GQLRE 179

                         170       180       190
                  ....*....|....*....|....*....|....
gi 1172384890 161 KVEELR*HLLKWGFTTP*KKHQKEPPFLWMGYEL 194
Cdd:cd01645   180 IYEELRQTLLRWGLTIPPEKVQKEPPFQYLGYEL 213

Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed of a four helix bundle.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1172384890 201 VQPIQLPDKDSWTVNDIQKLVGKLNWASQIY*--GI*I*QLCKLLRGAKALTDIVPLTAEAELELA 264
Cdd:pfam06817   1 PQKLQLRKDHLKTLNDFQKLLGDINWIRPYLGitTYDLKPLFSLLRGDSDLTSPRTLTEEAEEALQ 66

RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of single-stranded RNA into double-stranded viral DNA for integration into host chromosomes. Proteins in this subfamily contain long terminal repeats (LTRs) and are multifunctional enzymes with RNA-directed DNA polymerase, DNA directed DNA polymerase, and ribonuclease hybrid (RNase H) activities. The viral RNA genome enters the cytoplasm as part of a nucleoprotein complex, and the process of reverse transcription generates in the cytoplasm forming a linear DNA duplex via an intricate series of steps. This duplex DNA is colinear with its RNA template, but contains terminal duplications known as LTRs that are not present in viral RNA. It has been proposed that two specialized template switches, known as strand-transfer reactions or "jumps", are required to generate the LTRs.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172384890   1 MEKEGKISKIGpeNPYNTPVFAIKKKDS*KWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKK*SVTVLDVGDAYFSVPL 80
Cdd:cd01645    24 QLKEGHIEPST--SPWNTPVFVIKKKSG-KWRLLHDLRAVNAQTQDMGALQPGLPHPAALPKGWPLIVLDLKDCFFSIPL 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172384890  81 HEDFRKYTAFTIPSTNNETPGIRYQYNVLPQGWKGSPAIFQCSMTKILEPFRTQNPEIVIYQYMDDLYVGSDLEiGQHRK 160
Cdd:cd01645   101 HPDDRERFAFTVPSINNKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYPDIVIYHYMDDILIASDLE-GQLRE 179

                         170       180       190
                  ....*....|....*....|....*....|....
gi 1172384890 161 KVEELR*HLLKWGFTTP*KKHQKEPPFLWMGYEL 194
Cdd:cd01645   180 IYEELRQTLLRWGLTIPPEKVQKEPPFQYLGYEL 213

RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the intact endogenous retrovirus ZFERV from zebrafish and to Moloney murine leukemia virus RT. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs. Phylogenetic analysis suggests that ZFERV belongs to a distinct group of retroviruses.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172384890  15 PYNTPVFAIKKKDS*KWRKLVDFRELNKRTQDfweVQLGIPHPAGL-----KKK*SVTVLDVGDAYFSVPLHEDFRKYTA 89
Cdd:cd03715    36 PWNTPILPVKKPGGNDYRMVQDLRLVNQAVLP---IHPAVPNPYTLlsllpPKHQWYTVLDLANAFFSLPLAPDSQPLFA 112

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172384890  90 FTIPstnnetpGIRYQYNVLPQGWKGSPAIFQCSMTKILEPFRTQNPEIVIYQYMDDLYVGSDLEiGQHRKKVEELR*HL 169
Cdd:cd03715   113 FEWE-------GQQYTFTRLPQGFKNSPTLFHEALARDLAPFPLEHEGTILLQYVDDLLLAADSE-EDCLKGTDALLTHL 184

                         170
                  ....*....|...
gi 1172384890 170 LKWGFTTP*KKHQ 182
Cdd:cd03715   185 GELGYKVSPKKAQ 197

Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed of a four helix bundle.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1172384890 201 VQPIQLPDKDSWTVNDIQKLVGKLNWASQIY*--GI*I*QLCKLLRGAKALTDIVPLTAEAELELA 264
Cdd:pfam06817   1 PQKLQLRKDHLKTLNDFQKLLGDINWIRPYLGitTYDLKPLFSLLRGDSDLTSPRTLTEEAEEALQ 66

RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members of the subfamily include the Dictyostelium DIRS-1, Volvox carteri kangaroo, and Panagrellus redivivus PAT elements. These elements differ from LTR and conventional non-LTR retrotransposons. They contain split direct repeat (SDR) termini, and have been proposed to integrate via double-stranded closed-circle DNA intermediates assisted by an encoded recombinase which is similar to gamma-site-specific integrase.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172384890  69 LDVGDAYFSVPLHEDFRKYTAFtIPStnnetpGIRYQYNVLPQGWKGSPAIFqcsmTKILEP--FRTQNPEIVIYQYMDD 146
Cdd:cd03714     1 VDLKDAYFHIPILPRSRDLLGF-AWQ------GETYQFKALPFGLSLAPRVF----TKVVEAllAPLRLLGVRIFSYLDD 69

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1172384890 147 -LYVGSDLeigQHRKKVEELR*HLL--KWGFTTP*KKHQKEP 185
Cdd:cd03714    70 lLIIASSI---KTSEAVLRHLRATLlaNLGFTLNLEKSKLGP 108